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Old   November 22, 2022, 01:21
Unhappy Installing OpenFOAM on hpc
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leon
Join Date: Feb 2019
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nang19960916 is on a distinguished road
I am trying to install openfoam on a hpc and I do not have the sudo permission.
Quote:
-------------------------------------------------------------------------------
Shell: bash
Host: hpc2021
OS: Linux version 4.18.0-348.7.1.el8_5.x86_64

System check: PASS
==================
Can continue to OpenFOAM installation.

(base) foam
(base) ./Allwmake -s -l
Logging wmake -all output to 'log.linux64GccDPInt32Opt'

gcc=/usr/bin/gcc
clang=
mpirun=/share1/miniconda/py39/4.10.3/bin/mpirun
make=/usr/bin/make
cmake=
wmake=/home/cnwong22/openfoam/openfoam2206/wmake/wmake
m4=/usr/bin/m4
flex=/usr/bin/flex

compiler=/usr/bin/g++
g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-4)

========================================
Starting compile openfoam2206 Allwmake
Gcc system compiler []
linux64GccDPInt32Opt, with SYSTEMOPENMPI sys-openmpi
========================================

built wmake-bin (linux64Gcc)
Skip ThirdParty (no directory)
========================================
Compile OpenFOAM libraries
========================================
ln: OpenFOAM/lnInclude
ln: OSspecific/POSIX/lnInclude
found <sys/inotify.h> -- enabling inotify for file monitoring.
wmake libo (POSIX)
wmake dummy (mpi=SYSTEMOPENMPI)
wmake dummy
wmake mpi (mpi=SYSTEMOPENMPI:sys-openmpi)
wmake mpi
wmake OpenFOAM
wmake fileFormats
wmake surfMesh
wmake meshTools
wmake finiteArea
wmake finiteVolume
wmake mesh/blockMesh
wmake mesh/extrudeModel
wmake dynamicMesh
wmake genericPatchFields
wmake parallel/decompose/decompositionMethods
ln: decompositionMethods/lnInclude
ln: kahipDecomp/lnInclude
ln: metisDecomp/lnInclude
ln: scotchDecomp/lnInclude
ln: ptscotchDecomp/lnInclude
wmake scotchDecomp
wmake ptscotchDecomp
wmake metisDecomp
wmake kahipDecomp
wmake MGridGen
ln: fvOptions/lnInclude
wmake lagrangian/basic
wmake lagrangian/distributionModels
wmake decompositionMethods
wmake decompose
wmake faDecompose
==> skip kahip (disabled)
==> skip metis (no header)
==> skip scotch (no header)
==> skip scotch (no header)
wmake reconstruct
wmake faReconstruct
wmake distributed
wmake dynamicFvMesh
wmake topoChangerFvMesh
wmake sampling
wmake twoPhaseMixture
wmake interfaceProperties
wmake twoPhaseProperties
wmake incompressible
wmake compressible
wmake immiscibleIncompressibleTwoPhaseMixture
wmake geometricVoF
==> skip randomProcesses library (no FFTW)
wmake ODE
ln: thermophysicalProperties/lnInclude
wmake specie
wmake solidSpecie
wmake thermophysicalProperties
wmake basic
wmake reactionThermo
wmake laminarFlameSpeed
wmake chemistryModel
wmake barotropicCompressibilityModel
wmake SLGThermo
wmake solidThermo
wmake solidChemistryModel
wmake radiation
wmake turbulenceModels
wmake incompressible
wmake compressible
wmake schemes
ln: phaseIncompressible/lnInclude
ln: phaseCompressible/lnInclude
wmake combustionModels
ln: regionFaModels/lnInclude
ln: faOptions/lnInclude
ln: overset/lnInclude
wmake overset
wmake fvOptions
wmake fvMotionSolver
ln: blockMesh/lnInclude
wmake snappyHexMesh
wmake blockMesh
wmake extrudeModel
wmake libso renumberMethods
==> skip SloanRenumber (no boost)
==> skip zoltanRenumber (no library)
wmake pairPatchAgglomeration
wmake waveModels
wmake engine
wmake libso (conversion)
==> skip ccmio (no header)
==> skip optional libccm adapter
wmake saturationModels
wmake multiphaseSystem
wmake twoPhaseSystem
wmake twoPhaseCompressibleTurbulenceModels
wmake phasesSystem
wmake compressibleMultiPhaseTurbulenceModels
wmake multiphaseSystem
wmake twoPhaseSystem
wmake phaseCompressibleTurbulenceModels
wmake VoFphaseIncompressibleTurbulenceModels
wmake incompressibleInterPhaseTransportModel
wmake field
wmake forces
wmake initialisation
wmake utilities
wmake solvers
wmake phaseSystems
==> skip randomProcesses library (no FFTW)
wmake thermoTools

.
.
.
wmake interfaceTrackingFvMesh
========================================
Done OpenFOAM libraries
========================================
========================================
Compile OpenFOAM applications
========================================
wmake utilities
wmake doc
wmake finiteArea
make[1]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/finiteArea'
wmake checkFaMesh
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/finiteArea/checkFaMesh'
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/finiteArea/checkFaMesh'
.
.
.
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced'
wmake collapseEdges
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/collapseEdges'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/collapseEdges'
wmake combinePatchFaces
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/combinePatchFaces'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/combinePatchFaces'
wmake modifyMesh
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/modifyMesh'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/modifyMesh'
wmake PDRMesh
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/PDRMesh'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/PDRMesh'
wmake refineHexMesh
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/refineHexMesh'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/refineHexMesh'
wmake refinementLevel
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/refinementLevel'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/refinementLevel'
wmake refineWallLayer
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/refineWallLayer'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/refineWallLayer'
wmake removeFaces
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/removeFaces'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/removeFaces'
wmake selectCells
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/selectCells'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/selectCells'
wmake snappyRefineMesh
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/snappyRefineMesh'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/snappyRefineMesh'
wmake splitCells
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/splitCells'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced/splitCells'
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/advanced'
wmake conversion
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion'
wmake ansysToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/ansysToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/ansysToFoam'
wmake ccm
==> skip optional ccm conversion components (no libccm)
wmake cfx4ToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/cfx4ToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/cfx4ToFoam'
wmake datToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/datToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/datToFoam'
wmake fireToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/fireToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/fireToFoam'
wmake fluent3DMeshToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/fluent3DMeshToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/fluent3DMeshToFoam'
wmake fluentMeshToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/fluentMeshToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/fluentMeshToFoam'
wmake foamMeshToFluent
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/foamMeshToFluent'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/foamMeshToFluent'
wmake foamToFireMesh
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/foamToFireMesh'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/foamToFireMesh'
wmake foamToStarMesh
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/foamToStarMesh'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/foamToStarMesh'
wmake foamToSurface
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/foamToSurface'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/foamToSurface'
wmake gambitToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/gambitToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/gambitToFoam'
wmake gmshToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/gmshToFoam'
wmake gmsh
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/gmshToFoam'
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/gmshToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/gmshToFoam'
wmake ideasUnvToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/ideasUnvToFoam'
wmake unv
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/ideasUnvToFoam'
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/ideasUnvToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/ideasUnvToFoam'
wmake kivaToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/kivaToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/kivaToFoam'
wmake mshToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/mshToFoam'
wmake testFiles
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/mshToFoam'
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/mshToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/mshToFoam'
wmake netgenNeutralToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/netgenNeutralToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/netgenNeutralToFoam'
wmake plot3dToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/plot3dToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/plot3dToFoam'
wmake star4ToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/star4ToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/star4ToFoam'
wmake tetgenToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/tetgenToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/tetgenToFoam'
wmake vtkUnstructuredToFoam
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/vtkUnstructuredToFoam'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/vtkUnstructuredToFoam'
wmake writeMeshObj
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/writeMeshObj'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion/writeMeshObj'
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/conversion'
wmake doc
wmake generation
wmake PDRblockMesh
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/PDRblockMesh'
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/PDRblockMesh'
wmake blockMesh
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/blockMesh'
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/blockMesh'
wmake extrude
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude'
wmake extrudeMesh
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude/extrudeMesh'
wmake extrudedMesh
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude/extrudeMesh'
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude/extrudeMesh'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude/extrudeMesh'
wmake extrudeToRegionMesh
make[3]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude/extrudeToRegionMesh'
make[3]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude/extrudeToRegionMesh'
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude'
wmake extrude2DMesh
wmake extrude2DMesh
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude2DMesh/extrude2DMesh'
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude2DMesh/extrude2DMesh'
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude2DMesh/extrude2DMesh'
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude2DMesh/extrude2DMesh'
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude2DMesh'
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/extrude2DMesh'
wmake snappyHexMesh
make[2]: Entering directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/snappyHexMesh'
link: /home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/bin/snappyHexMesh
/usr/bin/ld: warning: libscotch-6.so, needed by /home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libscotcherrexit-6.so, needed by /home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so, not found (try using -rpath or -rpath-link)
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_graphInit'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_stratExit'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_graphCheck'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_randomReset'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_archInit'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_stratGraphMap'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_graphExit'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_graphMap'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_archExit'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_archCmpltw'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_graphBuild'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_stratInit'
/home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/lib/libscotchDecomp.so: undefined reference to `SCOTCH_archCmplt'
collect2: error: ld returned 1 exit status
make[2]: *** [/home/cnwong22/openfoam/openfoam2206/wmake/makefiles/general:150: /home/cnwong22/openfoam/openfoam2206/platforms/linux64GccDPInt32Opt/bin/snappyHexMesh] Error 1
make[2]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh/generation/snappyHexMesh'
make[1]: *** [/home/cnwong22/openfoam/openfoam2206/wmake/makefiles/apps:28: generation] Error 2
make[1]: Leaving directory '/home/cnwong22/openfoam/openfoam2206/applications/utilities/mesh'
make: *** [/home/cnwong22/openfoam/openfoam2206/wmake/makefiles/apps:28: mesh] Error 2
Done logging to 'log.linux64GccDPInt32Opt'
When I run snappyHexMesh, command is not found
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Old   November 25, 2022, 19:52
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Antony Ashley Raja B
Join Date: Jul 2015
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Are you sure if openfoam was installed in the first place? If installed you can check if you sourced the binaries.
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